Variant report

Variant	rs73405377
Chromosome Location	chr15:52030977-52030978
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr15:52030811-52030990	SK-N-SH	brain:	n/a	n/a
2	REST	chr15:52030706-52031178	MCF-7	breast:	n/a	n/a
3	REST	chr15:52030833-52031001	PANC-1	pancreas:	n/a	n/a
4	REST	chr15:52030741-52031065	A549	lung:	n/a	n/a
5	REST	chr15:52030714-52031082	U87	brain:	n/a	n/a
6	REST	chr15:52030604-52031122	K562	blood:	n/a	n/a
7	REST	chr15:52030707-52031180	PANC-1	pancreas:	n/a	n/a
8	REST	chr15:52030767-52031033	HepG2	liver:	n/a	n/a
9	REST	chr15:52030730-52031139	HCT-116	colon:	n/a	n/a
10	MXI1	chr15:52027409-52031724	SK-N-SH	brain:	n/a	n/a
11	REST	chr15:52030018-52031190	A549	lung:	n/a	chr15:52030058-52030068
12	REST	chr15:52030718-52031035	PANC-1	pancreas:	n/a	n/a
13	REST	chr15:52030680-52031116	SK-N-SH	brain:	n/a	n/a
14	REST	chr15:52030837-52031005	GM12878	blood:	n/a	n/a
15	RCOR1	chr15:52030745-52031101	K562	blood:	n/a	n/a
16	REST	chr15:52030769-52031087	PFSK-1	brain:	n/a	n/a
17	REST	chr15:52030752-52031089	HepG2	liver:	n/a	n/a
18	REST	chr15:52030765-52031061	H1-hESC	embryonic stem cell:	n/a	n/a
19	REST	chr15:52030716-52031079	H1-hESC	embryonic stem cell:	n/a	n/a
20	REST	chr15:52030809-52030999	U87	brain:	n/a	n/a
21	REST	chr15:52030739-52031035	K562	blood:	n/a	n/a
22	REST	chr15:52030496-52031236	ECC-1	luminal epithelium:	n/a	n/a
23	REST	chr15:52030682-52031067	PFSK-1	brain:	n/a	n/a
24	REST	chr15:52030793-52031002	U87	brain:	n/a	n/a
25	REST	chr15:52030537-52031198	ECC-1	luminal epithelium:	n/a	n/a
26	GATA1	chr15:52030505-52031810	PBDE	blood:	n/a	chr15:52030719-52030726 chr15:52030717-52030729 chr15:52030719-52030728 chr15:52030712-52030733 chr15:52030719-52030726 chr15:52030715-52030731 chr15:52030718-52030728 chr15:52030715-52030731 chr15:52030719-52030726 chr15:52030717-52030730 chr15:52030720-52030737
27	REST	chr15:52030724-52031105	HL-60	blood:	n/a	n/a
28	REST	chr15:52030790-52031041	Hela-S3	cervix:	n/a	n/a
29	REST	chr15:52030346-52031253	PFSK-1	brain:	n/a	n/a
30	REST	chr15:52030774-52031022	SK-N-SH	brain:	n/a	n/a
31	REST	chr15:52030358-52031222	MCF-7	breast:	n/a	n/a
32	REST	chr15:52030712-52031082	U87	brain:	n/a	n/a
33	REST	chr15:52030680-52031143	Hela-S3	cervix:	n/a	n/a
34	REST	chr15:52030552-52031155	PANC-1	pancreas:	n/a	n/a
35	REST	chr15:52030523-52031239	HL-60	blood:	n/a	n/a
36	REST	chr15:52030801-52030998	HepG2	liver:	n/a	n/a
37	REST	chr15:52030644-52031123	GM12878	blood:	n/a	n/a
38	REST	chr15:52030775-52031051	HCT-116	colon:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52029378..52032499-chr15:52121077..52123299,3	MCF-7	breast:
2	chr15:52028180..52031136-chr15:52040562..52045385,6	MCF-7	breast:
3	chr15:52005662..52007756-chr15:52028876..52031424,2	MCF-7	breast:
4	chr15:52029435..52031649-chr15:52311154..52313570,2	K562	blood:
5	chr15:52029591..52032408-chr15:52042418..52044684,3	K562	blood:
6	chr15:52030561..52031125-chr15:52068898..52069830,2	K562	blood:
7	chr15:52027363..52032665-chr15:52041435..52046045,23	MCF-7	breast:
8	chr15:51911576..51916583-chr15:52027382..52031699,5	MCF-7	breast:
9	chr12:64614231..64616104-chr15:52029344..52031052,2	MCF-7	breast:
10	chr15:52030420..52032691-chr15:52120807..52123246,2	MCF-7	breast:
11	chr15:52028355..52032748-chr15:52040539..52046492,10	K562	blood:

No data

Variant related genes	Relation type
LYSMD2	TF binding region
ENSG00000259377	Chromatin interaction
ENSG00000138594	Chromatin interaction
ENSG00000104093	Chromatin interaction
ENSG00000128872	Chromatin interaction
ENSG00000259296	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000259438	Chromatin interaction
ENSG00000174206	Chromatin interaction
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10519324	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16953079	1.00[EUR][1000 genomes]
rs16964509	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16964513	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16964517	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16964530	1.00[EUR][1000 genomes]
rs17648915	0.95[AFR][1000 genomes]
rs17648927	0.95[AFR][1000 genomes]
rs17649601	1.00[EUR][1000 genomes]
rs17705437	0.95[AFR][1000 genomes]
rs2554357	1.00[EUR][1000 genomes]
rs57399438	0.95[AFR][1000 genomes]
rs58356723	1.00[EUR][1000 genomes]
rs58434025	0.95[AFR][1000 genomes]
rs58559761	0.95[AFR][1000 genomes]
rs58958163	1.00[EUR][1000 genomes]
rs59426894	0.95[AFR][1000 genomes]
rs59522140	1.00[EUR][1000 genomes]
rs60590663	0.95[AFR][1000 genomes]
rs73405314	0.95[AFR][1000 genomes]
rs73405317	0.95[AFR][1000 genomes]
rs73405321	0.95[AFR][1000 genomes]
rs73405322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73405324	0.95[AFR][1000 genomes]
rs73405338	0.95[AFR][1000 genomes]
rs73405339	0.95[AFR][1000 genomes]
rs73405346	0.95[AFR][1000 genomes]
rs73405351	0.95[AFR][1000 genomes]
rs73405368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73405370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73405389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73405400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407332	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407384	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407392	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407393	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73409029	1.00[EUR][1000 genomes]
rs73409034	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830011	chr15:52027777-52048710	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
2	esv3322785	chr15:52028185-52031033	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
3	esv3433188	chr15:52028510-52031058	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
4	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52030200-52031000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr15:52030200-52031000	Active TSS	Fetal Kidney	kidney
3	chr15:52030200-52031000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr15:52030200-52031000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr15:52030200-52031000	Flanking Active TSS	GM12878-XiMat	blood
6	chr15:52030200-52031400	Enhancers	Fetal Heart	heart
7	chr15:52030200-52032000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:52030400-52031000	Enhancers	Primary hematopoietic stem cells	blood
9	chr15:52030400-52031000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr15:52030400-52031000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr15:52030400-52031000	Enhancers	Fetal Intestine Large	intestine
12	chr15:52030400-52031000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr15:52030400-52031000	Bivalent Enhancer	Fetal Stomach	stomach
14	chr15:52030400-52031000	Enhancers	Left Ventricle	heart
15	chr15:52030400-52031000	Enhancers	Right Ventricle	heart
16	chr15:52030600-52031000	Enhancers	Primary B cells from peripheral blood	blood
17	chr15:52030600-52031000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr15:52030600-52031000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr15:52030600-52031000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:52030600-52031000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:52030600-52031000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr15:52030600-52031000	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr15:52030600-52031000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr15:52030600-52031000	Enhancers	Liver	Liver
25	chr15:52030600-52031000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr15:52030600-52031000	Enhancers	Colon Smooth Muscle	Colon
27	chr15:52030600-52031000	Enhancers	Pancreas	Pancrea
28	chr15:52030600-52031000	Enhancers	Hela-S3	cervix
29	chr15:52030600-52031200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
30	chr15:52030600-52031200	Enhancers	Fetal Muscle Leg	muscle
31	chr15:52030600-52031200	Enhancers	Fetal Thymus	thymus
32	chr15:52030600-52031200	Enhancers	Dnd41	blood
33	chr15:52030600-52031200	Enhancers	Osteobl	bone
34	chr15:52030600-52031400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:52030600-52031400	Enhancers	Brain Angular Gyrus	brain
36	chr15:52030600-52031600	Enhancers	Brain Anterior Caudate	brain
37	chr15:52030600-52031800	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr15:52030600-52031800	Weak transcription	Thymus	Thymus
39	chr15:52030600-52031800	Enhancers	HMEC	breast
40	chr15:52030600-52032000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:52030600-52032000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr15:52030600-52032000	Enhancers	NHEK	skin
43	chr15:52030600-52032600	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr15:52030600-52032800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:52030600-52043200	Weak transcription	Gastric	stomach
46	chr15:52030800-52031000	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr15:52030800-52031000	Enhancers	Brain Substantia Nigra	brain
48	chr15:52030800-52031000	Enhancers	Fetal Brain Male	brain
49	chr15:52030800-52031000	Enhancers	A549	lung
50	chr15:52030800-52031200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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